SMTL ID : 5n2w.1

WT-Parkin and pUB complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-1-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.193, H.197, C.229, C.233 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.193, A:H.197, A:C.229, A:C.233 ZN.2: 5 residues within 4Å: Chain A: R.288, C.305, C.308, H.313, C.317 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.305, A:C.308, A:H.313, A:C.317 ZN.3: 4 residues within 4Å: Chain A: C.386, C.389, C.397, H.401 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.386, A:C.389, A:C.397, A:H.401 ZN.4: 5 residues within 4Å: Chain A: C.106, T.108, C.109, C.136, C.141 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.106, A:C.109, A:C.136, A:C.141 ZN.5: 4 residues within 4Å: Chain A: C.178, C.181, C.200, C.203 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.178, A:C.181, A:C.200, A:C.203 ZN.6: 4 residues within 4Å: Chain A: C.272, C.277, C.292, C.300 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.272, A:C.277, A:C.292, A:C.300 ZN.7: 4 residues within 4Å: Chain A: C.358, C.361, C.376, C.381 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.358, A:C.361, A:C.376, A:C.381 ZN.8: 4 residues within 4Å: Chain A: C.90, C.94, C.152, H.155 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.90, A:C.94, A:C.152, A:H.155

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 6 residues within 4Å: Chain A: T.177, C.178, T.182, A.337, Q.340, A.341 Ligand excluded by PLIP

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.10: 4 residues within 4Å: Chain A: V.126, L.127, E.147, F.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.148, A:F.148 TMO.11: 8 residues within 4Å: Chain A: G.47, H.68, T.210, R.211, D.214, Q.329, A.330, Y.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.329 Salt bridges: A:D.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-04-19

Peptides

E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin: A
Polyubiquitin-B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin

Polyubiquitin-B

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